[English] 日本語
Yorodumi
- PDB-1mke: Structure of the N-WASP EVH1 Domain-WIP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mke
TitleStructure of the N-WASP EVH1 Domain-WIP complex
ComponentsFusion protein consisting of Wiskott-Aldrich syndrome protein interacting protein (WIP), GSGSG linker, and Neural Wiskott-Aldrich syndrome protein (N-WASP)
KeywordsPROTEIN BINDING / polyproline / protein-protein complex
Function / homology
Function and homology information


negative regulation of membrane tubulation / spindle localization / membrane invagination / positive regulation of clathrin-dependent endocytosis / plasma membrane tubulation / postsynaptic actin cytoskeleton organization / postsynapse organization / negative regulation of lymphocyte migration / vesicle transport along actin filament / regulation of cell projection assembly ...negative regulation of membrane tubulation / spindle localization / membrane invagination / positive regulation of clathrin-dependent endocytosis / plasma membrane tubulation / postsynaptic actin cytoskeleton organization / postsynapse organization / negative regulation of lymphocyte migration / vesicle transport along actin filament / regulation of cell projection assembly / actin cap / profilin binding / actin filament-based movement / vesicle organization / cytoskeletal anchor activity / positive regulation of chemotaxis / vesicle budding from membrane / response to other organism / dendritic spine morphogenesis / actin polymerization or depolymerization / protein-containing complex localization / regulation of postsynapse organization / positive regulation of filopodium assembly / cell leading edge / CDC42 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / cytoskeletal protein binding / ruffle / actin filament polymerization / RAC1 GTPase cycle / protein folding chaperone / actin filament / FCGR3A-mediated phagocytosis / response to bacterium / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / actin cytoskeleton / lamellipodium / regulation of protein localization / actin binding / actin cytoskeleton organization / protein-containing complex assembly / cytoplasmic vesicle / postsynapse / Golgi membrane / cell division / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain profile. ...: / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain profile. / WH2 domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Actin nucleation-promoting factor WASL / WAS/WASL-interacting protein family member 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsVolkman, B.F. / Prehoda, K.E. / Scott, J.A. / Peterson, F.C. / Lim, W.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Structure of the N-WASP EVH1 Domain-WIP Complex. Insight into the Molecular Basis of Wiskott-Aldrich Syndrome.
Authors: Volkman, B.F. / Prehoda, K.E. / Scott, J.A. / Peterson, F.C. / Lim, W.A.
History
DepositionAug 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fusion protein consisting of Wiskott-Aldrich syndrome protein interacting protein (WIP), GSGSG linker, and Neural Wiskott-Aldrich syndrome protein (N-WASP)


Theoretical massNumber of molelcules
Total (without water)17,4231
Polymers17,4231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 50LOWEST TARGET FUNCTION
RepresentativeModel #1minimized average structure

-
Components

#1: Protein Fusion protein consisting of Wiskott-Aldrich syndrome protein interacting protein (WIP), GSGSG linker, and Neural Wiskott-Aldrich syndrome protein (N-WASP) / WIP - N-WASP


Mass: 17422.832 Da / Num. of mol.: 1 / Fragment: WIP peptide and N-WASP EVH1 domain
Source method: isolated from a genetically manipulated source
Details: FUSION PROTEIN COMPRISES RESIDUES 461-485 of WIP, a GSGSG linker sequence, and residues 26-147 (EVH1 domain) of N-WASP
Source: (gene. exp.) Rattus norvegicus, Homo sapiens / Genus: Rattus, Homo / Species: , / Strain: , / Plasmid: pBH4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43516, UniProt: O08816

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
NMR detailsText: REPRESENTATIVE CONFORMER (MODEL 1) IS MINIMIZED AVERAGE STRUCTURE.

-
Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N protein 20 mM PO4 buffer 1 mM dithiothreitol90% H2O/10% D2O
2U-13C/15N protein 20 mM PO4 buffer 1 mM dithiothreitol90% H2O/10% D2O
Sample conditionsIonic strength: 20 mM NaCl / pH: 7 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentert, P.structure solution
XwinNMR3Brukercollection
XEASY1.3Guentert, P.data analysis
NMRPipeDelaglio, F.processing
DYANA1.5Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: final structures were derived from a total of 1884 non-trivial NOE distance constraints, including 135 restraints between residues of the WIP peptide and the EVH1 domain. 143 phi and psi ...Details: final structures were derived from a total of 1884 non-trivial NOE distance constraints, including 135 restraints between residues of the WIP peptide and the EVH1 domain. 143 phi and psi torsion angle constraints were generated from chemical shift database searching using the program TALOS
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: LOWEST TARGET FUNCTION / Conformers calculated total number: 50 / Conformers submitted total number: 21

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more